Nothing
`plot.mefa` <-
function(x, stat=1:4, type=c("hist", "rank"), trafo=c("none", "log",
"ratio"), show=TRUE, ylab, xlab, ...)
{
if (missing(ylab))
ylab <- NULL
if (missing(xlab))
xlab <- NULL
if (!all(stat %in% 1:4))
stop("'stat' must be in 1:4")
if (!length(stat) == 1) stat <- 1
if (!length(type) == 1) type <- type[1]
if (!length(trafo) == 1) trafo <- trafo[1]
trafo <- match.arg(trafo, c("none", "log", "ratio"))
## maintaining back compatibility
type <- match.arg(type, c("hist", "rank", "bar"))
if (type == "hist")
type <- "bar"
if (!is.null(ylab))
ylab2 <- ylab
if (!is.null(xlab))
xlab2 <- xlab
if (is.null(ylab) && type=="bar")
ylab2 <- "Frequency"
if (is.null(ylab) && type=="rank")
ylab2 <- "Rank"
if (stat == 1) {
if (is.null(ylab)) ylab2 <- paste(ylab2, "(samples)")
if (is.null(xlab)) xlab2 <- "Number of taxa"
}
if (stat == 2) {
if (is.null(ylab)) ylab2 <- paste(ylab2, "(samples)")
if (is.null(xlab)) xlab2 <- "Number of individuals"
}
if (stat == 3) {
if (is.null(ylab)) ylab2 <- paste(ylab2, "(taxa)")
if (is.null(xlab)) xlab2 <- "Frequency of occurrence"
}
if (stat == 4) {
if (is.null(ylab)) ylab2 <- paste(ylab2, "(taxa)")
if (is.null(xlab)) xlab2 <- "Abundance"
}
yvar <- summary(x)[[stat]]
if (trafo=="log") {
yvar <- log10(yvar)
if (is.null(ylab) && type=="bar")
ylab2 <- paste("log10", ylab2)
if (is.null(ylab) && type=="rank")
xlab2 <- paste("log10", xlab2)}
if (trafo=="ratio") {
yvar <- yvar / max(yvar)
if (is.null(ylab) && type=="bar")
ylab2 <- paste("Relative", tolower(ylab2))
if (is.null(ylab) && type=="rank")
xlab2 <- paste("Relative", tolower(xlab2))}
if (type=="bar") {
if (all(as.integer(yvar) == as.numeric(yvar))) {
yvar <- table(yvar)
if (show)
plot(yvar, xlab=xlab2, ylab=ylab2, ...)
} else {
hist(yvar, xlab=xlab2, ylab=ylab2, ...)
}
}
if (type=="rank") {
yvar <- yvar[order(yvar, decreasing=TRUE)]
if (show)
plot(yvar, type="l", xlab=ylab2, ylab=xlab2, ...)}
if (show)
invisible(yvar) else return(yvar)
}
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